Difference between revisions of "Jeff Kinne"

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This page is maintained by me, Jeff Kinne. I am a professor of computer science at Indiana State University. I have taught just about every CS course that we offer at the BS and MS levels. I was trained in computational complexity (within theoretical computer science) and continue to be interested in this year. Since maybe 2015 or so, most of my research work has been in bioinformatics. If you want a laundry list of things I have done, you can see my [https://docs.google.com/document/d/1Z5ms6PFZH9H_dUcPF35VNS3u3IYnV2jlxagJVfJ9huE/edit#heading=h.h9dbt25tdl7r C.V.] (aka resume).
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This page is maintained by me, Jeff Kinne. I am a professor of computer science at Indiana State University. I have taught just about every CS course that we offer at the BS and MS levels. I was trained in computational complexity (within theoretical computer science) during my PhD studies and continue to be interested in this year. Since maybe 2015 or so, most of my research work has been in bioinformatics. If you want a laundry list of things I have done, you can see my [https://docs.google.com/document/d/1Z5ms6PFZH9H_dUcPF35VNS3u3IYnV2jlxagJVfJ9huE/edit#heading=h.h9dbt25tdl7r C.V.] (aka resume).
  
 
==Contact==
 
==Contact==
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I am currently in the midst of moving from Root Hall to Technology Center. My email address will not change, and I believe my phone number should stay the same as well.
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I am currently in the midst of moving from Root Hall to Technology Center at ISU. My email address will not change, and I believe my phone number should stay the same as well.
  
 
'''Email''': [http://mailto:jkinne@indstate.edu jkinne@indstate.edu] (also jkinne@cs.indstate.edu and jeffrey.kinne@indstate.edu all go to the same place).
 
'''Email''': [http://mailto:jkinne@indstate.edu jkinne@indstate.edu] (also jkinne@cs.indstate.edu and jeffrey.kinne@indstate.edu all go to the same place).
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'''Phone''': office phone - 812-237-2126.  
 
'''Phone''': office phone - 812-237-2126.  
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'''Office''': within the ECET office suite, TC 301
 
'''Office''': within the ECET office suite, TC 301
  
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ISU uses Teams and Zoom for virtual meetings. I am happy to meet on other platforms as well (Google meet, WebEx, Skype, etc.).
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'''Virtual meetings''': ISU uses Teams and Zoom. I am happy to meet on other platforms as well (Google meet, WebEx, Skype, etc.).
  
 
'''Schedule a meeting''': https://cs.indstate.edu/jkinne-meeting
 
'''Schedule a meeting''': https://cs.indstate.edu/jkinne-meeting
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==Research==
 
==Research==
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'''Author ordering''' In CS and mathematics, author ordering is normally alphabetical (so you cannot tell who is the primary author just by looking at the author list). In biology / bioinformatics, author ordering is normally in order of who contributed the most - normally the primary author is listed first, and the director of the laboratory that paid for the research is listed last. Many papers published recently have a statement on author contributions (who did what, etc.) at the end of the paper.
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'''Current projects''' Projects that I am still actively working on from among those listed below include: differential gene expression analysis, transcription factor binding site analysis, and gene expression analysis in cichlids. For other completed projects, there is always the possibility to improve the results or apply techniques to a new setting.
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===Posters===
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''Differential gene expression analysis'' -
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[https://cs.indstate.edu/info/posters/bd4isu2022-bartlett.pdf 2022 BD4ISU/SURE],
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[https://cs.indstate.edu/info/posters/IAS_Poster-Schwab.pdf 2019 Indiana Academy of Sciences],
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[https://cs.indstate.edu/info/posters/icibm2019-tally-.pdf 2019 ICIBM],
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[https://cs.indstate.edu/info/posters/bd4isu2019-alvarezdubon-kaur.pdf 2019 BD4ISU/SURE],
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[https://cs.indstate.edu/info/posters/bd4isu2018-tally-alvarez.pdf 2018 BD4ISU/SURE],
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[https://cs.indstate.edu/info/posters/surf2018-revesz-knight.pdf 2018 SURF],
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[https://cs.indstate.edu/info/posters/sure2018-williamson.pdf 2018 SURE]
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''Transcription factor binding site analysis'' -
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[https://cs.indstate.edu/info/posters/bd4isu2022-hoffman.pdf 2022 BD4ISU/SURE],
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[https://cs.indstate.edu/info/posters/bd4isu2019-bennet-bigler.pdf 2019 BD4ISU/SURE]
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''Transmembrane protein search in prokaryotes'' -
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[https://cs.indstate.edu/info/posters/bd4isu2021-hoffman.pdf 2021 BD4ISU/SURE]
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''Predicting Drug-Gene Interactions'' -
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[https://cs.indstate.edu/info/posters/bd4isu2020-bennett.pdf 2020 BD4ISU/SURE]
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''Gene expression analysis in cichlids'' -
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[https://cs.indstate.edu/info/posters/bd4isu2021-gosnell.pdf 2021 BD4ISU/SURE],
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[https://cs.indstate.edu/info/posters/bd4isu2020-gosnell-sagarsee.pdf 2020 BD4ISU/SURE]
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''3d printing'' -
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[https://cs.indstate.edu/info/posters/sure2016-golish-watts.pdf 2016 SURE]
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''Large prime searches'' -
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[https://cs.indstate.edu/info/posters/sure2014-xiang.pdf (2014],
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[https://cs.indstate.edu/info/posters/sure2013-salman-toure.pdf 2013 SURE],
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[https://cs.indstate.edu/info/posters/csui2013-salman-toure.pdf 2013 CSUI]
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===Publication list===
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Tara Hoffman, Jeff Kinne, Kyu Hong Cho. Pro-SMP finder-A systematic approach for discovering small membrane proteins in prokaryotes. PLoS One. 2024 Feb 29;19(2):e0299169. [https://dx.plos.org/10.1371/journal.pone.0299169. full text], [https://cs.indstate.edu/pro-smp-finder pipeline].
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Jeff Kinne, Akbar Rafiey, Arash Rafiey, Mohammad Sorkhpar. Vertex Ordering with Precedence Constraints. In: Fernau, H., Jansen, K. (eds) Fundamentals of Computation Theory. FCT 2023. Lecture Notes in Computer Science, vol 14292. Springer, Cham. [https://doi.org/10.1007/978-3-031-43587-4_22 DOI].
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Nick Gabry, Jeff Kinne, and Rusty Gonser. MetaPlex: An Ion Torrent COI metabarcoding workflow and toolkit to increase experimental efficacy and efficiency. [https://doi.org/10.22541/au.166322714.48673632/v1 manuscript], [https://github.com/NGabry/MetaPlex source code].
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Timothy J. Divoll, Veronica A. Brown, Jeff Kinne, Gary F. McCracken and Joy M. O'Keefe. Disparities in second-generation DNA metabarcoding results exposed with accessible and repeatable workflows. Molecular Ecology Resources, 2018. [https://onlinelibrary.wiley.com/doi/abs/10.1111/1755-0998.12770 abstract], [https://github.com/tdivoll/Bat-Diet-Metabarcoding source code].
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Yongsheng Bai, Jeff Kinne, Lizhong Ding, Ethan Rath, Aaron Cox, Siva Naidu and Youping Deng. Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly. BMC Bioinformatics, 18(Suppl 11):382, 2017.  [https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1801-y full text], [https://docs.google.com/presentation/d/1KtcMnQgTUsoFvKGxOGlOLtWa8Dypkyd7LhuF1K0z4Y0/edit?usp=sharing presentation (for ugrad CS majors)], [https://github.com/kinnejeff/read-split-fly source code], presented at ICIBM 2016.
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Yongsheng Bai, Jeff Kinne, Brandon Donham, Feng Jiang, Lizhong Ding, Justin R. Hassler, and Randal J. Kaufman. Read-Split-Run: An improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data. BMC Genomics 17(Suppl 7):503, 2016. [https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-2896-7 full text],  [https://github.com/xuric/read-split-run source code], presented at ICIBM 2015.
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Ruiwen Chen, Valentine Kabanets, and Jeff Kinne. Lower Bounds against Weakly-Uniform Threshold Circuits. In special issue of Algorithmica for invited papers from the the 18th International Computing and Combinatorics Conference (COCOON), Volume 17, issue 1, pages 47-75, 2014, doi:10.1007/s00453-013-9823-y.  [http://cs.indstate.edu/~jkinne/research/CKK.pdf draft PDF], [http://eccc.hpi-web.de/report/2012/007/#revision1 ECCC report].
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Jeff Kinne. On TC0 Lower Bounds for the Permanent. In Proceedings of the 18th International Computing and Combinatorics Conference (COCOON), LNCS 7434, pages 420-432, 2012.  [http://cs.indstate.edu/~jkinne/research/perm-tc0.pdf draft PDF], [http://cs.indstate.edu/~jkinne/talks/COCOON2012.pdf presentation].
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George Karakostas, Jeff Kinne, Dieter van Melkebeek. On Derandomization and Average-Case Complexity of Monotone Functions. In Theoretical Computer Science, volume 434, pages 35-44, 2012. [http://cs.indstate.edu/~jkinne/research/mon.pdf draft PDF]
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Jeff Kinne, Dieter van Melkebeek, and Ronen Shaltiel. Pseudorandom Generators, Typically-Correct Derandomization, and Circuit Lower Bounds. In the special issue of Computational Complexity for selected papers from The 13th International Workshop on Randomization and Computation (RANDOM), Volume 21, number 1, pages 3-61, 2012.  [http://cs.indstate.edu/~jkinne/research/KvMS.pdf draft PDF], [http://eccc.uni-trier.de/report/2010/129/ ECCC report].
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Jeff Kinne. Deterministic Simulations and Hierarchy Theorems for Randomized Algorithms. Ph.D. dissertation from the Computer Sciences department at the University of Wisconsin-Madison, 2010. [http://cs.indstate.edu/~jkinne/research/Jeff-Kinne-thesis.pdf PDF], [http://cs.indstate.edu/~jkinne/talks/Jeff-Kinne-defense.pdf presentation].
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Jeff Kinne and Dieter van Melkebeek. Space Hierarchy Results for Randomized and Other Semantic Models. In Computational Complexity volume 19, number 3, 2010, pages 423-475.  [http://cs.indstate.edu/~jkinne/research/KM-space-hierarchies-CC.pdf draft PDF], [http://eccc.hpi-web.de/eccc-reports/2007/TR07-134/index.html ECCC report].
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Jeff Kinne, Dieter van Melkebeek, and Ronen Shaltiel. Pseudorandom Generators and Typically-Correct Derandomization. In Proceedings of the 13th International Workshop on Randomization and Computation (RANDOM), LNCS 5687, pages 574-587, 2009. [http://cs.indstate.edu/~jkinne/research/KvMS_derand_RANDOM09.pdf PDF],  [http://cs.indstate.edu/~jkinne/talks/typ-correct-derand.ppt presentation].
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Jeff Kinne and Dieter van Melkebeek. Space Hierarchy Results for Randomized Models. In Proceedings of the 25th International Symposium on Theoretical Aspects of Computer Science (STACS), pages 433-444, 2008.  [http://cs.indstate.edu/~jkinne/research/space-hierarchies-STACS2008.pdf PDF], [http://cs.indstate.edu/~jkinne/talks/jkinne-STACS2008-presentation-web.pps presentation].
  
 
==Teaching==
 
==Teaching==
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For some of my recent thoughts on teaching, see [https://docs.google.com/document/d/1fnNjQ6comNXZ8c_UwsDVLN2TUcp9tJovfF0tqyAdFe8/edit?usp=sharing teaching thoughts]. I tend to update that once a year or few.
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And here is the laundry list of links to course websites...
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===Indiana State University===
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'''Summer Honors (high school)''' -
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[https://docs.google.com/document/d/13_NUmSFZ09gXjRUmwAmL-HWUgTFz6Hmo1KxbU7YZRtY/edit?usp=sharing Arificial Intelligence (2017)]
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'''GH 101 Computing and Data Science''' -
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[https://cs.indstate.edu/~jkinne/cs101-f2021 fall 2021],
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[https://docs.google.com/document/d/1BbmHvR47jKPkmNzi8J6EYxis0zKYlmLx5GK_2umti3E/edit?usp=sharing fall 2018]
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'''CS 151 Introduction to Programming''' -
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[https://cs.indstate.edu/cs151 spring 2024], [https://cs.indstate.edu/wiki/index.php/CS_151_Fall_2023 fall 2023], [http://cs.indstate.edu/~jkinne/cs151-su2020 summer 2020], [http://cs.indstate.edu/~jkinne/cs151-s2020 spring 2020], [http://cs.indstate.edu/~jkinne/cs151-f2019 fall 2019], [https://docs.google.com/document/d/1VEWRjgIMCfVNs_j4RvBGbLcERl7Q02zP_235LFm5DJE/edit?usp=sharing summer 2017] [https://docs.google.com/document/d/1i5BpZicaiHu2Zlaqalkc5_wLuxvoVI-OFzAW2KdIxz8/edit?usp=sharing fall 2014], [http://cs.indstate.edu/~jkinne/cs151-s2014 spring 2014], [http://cs.indstate.edu/~jkinne/cs151-f2013 fall 2013],
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[http://cs.indstate.edu/~jkinne/cs151-s2013 spring 2013 sections 001 and 003], [http://cs.indstate.edu/~jkinne/cs151-f2012 fall 2012 section 001], [http://cs.indstate.edu/~jkinne/cs151-s2012 spring 2012 sections 001 and 003], [http://cs.indstate.edu/~jkinne/cs151-f2011 fall 2011 sections 001 and 002],
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[http://cs.indstate.edu/~jkinne/cs151-s2011 spring 2011 section 003], [http://cs.indstate.edu/~jkinne/cs151-f2010 fall 2010 section 003]
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'''CS 170 Web Programming I''' -
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[https://docs.google.com/document/d/1LpYfGDfj5UAGdRDBuIkqJRx0v9GDvkzmfQSxjto5ez8/edit?usp=sharing Summer 2016]
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'''CS 201 Computer Science I''' -
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[https://docs.google.com/document/d/10N9tS-9aKqBMfd46XjtdUbS0UxXP6x4B9LNpP68rRtg/edit?usp=sharing Summer 2016],
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[https://docs.google.com/document/d/1RqUrbIYWtuBRgnNlf1RQNrhttuKZTYjT_q5hBxlScCk/edit?usp=sharing spring 2015],
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[http://cs.indstate.edu/~jkinne/cs201-s2014 spring 2014]
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'''CS 203 (formerly 303) Discrete Structures and Computing Theory''' -
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[https://cs.indstate.edu/wiki/index.php/CS_203 spring 2024],
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[https://cs.indstate.edu/wiki/index.php/CS_203_Fall_2024 fall 2023], [https://cs.indstate.edu/wiki/index.php/CS_303_Spring_2023 spring 2023], [https://cs.indstate.edu/wiki/index.php/CS_303_Fall_2022 fall 2022],
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'''CS 220 Java Programming''' -
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[https://docs.google.com/document/d/11WUUvp8mwWOL0i8Et5t-Glsyu61iJAZz0njo78ZAzpg/edit?usp=sharing spring 2015]
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'''CS 302 (formerly 202) Computer Science II''' -
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[http://cs.indstate.edu/~jkinne/cs202-f2020 fall 2020],
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[http://cs.indstate.edu/~jkinne/cs202-f2019/ fall 2019],
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[https://docs.google.com/document/d/1z5FkzB_ttV0K1gfqZM194wHEDZ-wx5I_ovBiI4etJp8/edit?usp=sharing fall 2017],
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[https://docs.google.com/document/d/1cAYqtdLtO5fCmiore0utezzpTRsxddfDWLcXi2yhmn0/edit?usp=sharing spring 2017],
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[https://docs.google.com/document/d/1QadsJAAQgscX6I13gDF6HloHY3-hX2AX_6oa0TwSs3E/edit?usp=sharing spring 2016]
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'''CS 420/520 Theory of Computation''' -
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[http://cs.indstate.edu/~jkinne/cs420-s2019/index.html spring 2019],
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[https://docs.google.com/document/d/1JzBW5D2nuXiPNLAvvr2UNaYJvkV9vvn6241MmbqLNl8/edit?usp=sharing fall 2016],
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[https://docs.google.com/document/d/1qxGwx9a_5BZyTt5eJeSxutCYUZ-tbvvWW2FLB1yVdTM/edit?usp=sharing fall 2015]
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'''CS 440/540 Graphics Programming''' -
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[http://cs.indstate.edu/~jkinne/cs440-f2012 fall 2012]
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'''CS 457/557 Database Processing''' -
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[http://cs.indstate.edu/~jkinne/cs457-f2012 fall 2012]
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'''CS 458/558 Algorithms''' -
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[http://cs.indstate.edu/~jkinne/cs458-f2020 fall 2020],
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[http://cs.indstate.edu/~jkinne/cs458-f2013/ fall 2013]
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'''CS 459/559 Topics in Computer Science''' -
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[http://cs.indstate.edu/~jkinne/bd4isu-summer-2019/ BD4ISU Summer 2019],
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[http://cs.indstate.edu/~jkinne/cs459-bd4isu-s2019/ BD4ISU Bioinformatics Programming, Spring 2019],
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[https://docs.google.com/document/d/1mzYcEOwY0_FPybYhXVZwszgHYRXK6k8yrQAqgEhjaBg/edit?usp=sharing Computational Software Packages and Tools, Summer I 2014]
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'''CS 469/569 Unix/Linux Administration and Networking''' -
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[https://cs.indstate.edu/~jkinne/cs469-s2022 spring 2022]
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'''CS 471/571 Operating Systems''' -
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[https://docs.google.com/document/d/1w2bGyWU5YWTlb4hvEJlIa5cAlKsbaOcKoACBGC8F-Is/edit?usp=sharing Fall 2018]
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'''CS 473/573 Computer Networks''' -
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[http://cs.indstate.edu/~jkinne/cs473-f2021 fall 2021],
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[http://cs.indstate.edu/~jkinne/cs473-s2021 spring 2021],
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[http://cs.indstate.edu/~jkinne/cs473-s2020 spring 2020],
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[https://docs.google.com/document/d/1ObUd5k_iIVWf28LeZYUfBlNjzCLA87zBbM0US5aa5pY/edit?usp=sharing spring 2015]
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'''CS 475/575 Artificial Intelligence''' -
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[http://cs.indstate.edu/~jkinne/cs475-f2011/ fall 2011]
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'''CS 499 Senior Seminar''' -
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[http://cs.indstate.edu/~jkinne/cs499-f2020 fall 2020],
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[http://cs.indstate.edu/~jkinne/cs499-f2019 fall 2019],
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[https://docs.google.com/document/d/1p-v_b9Nr4bxCXGVX4rk4TJbdaMgFa9qkLutopfKcfmE/edit?usp=sharing information]
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'''CS 500 Programming Fundamentals''' -
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[https://cs.indstate.edu/wiki/index.php/CS_500 spring 2024],
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[https://cs.indstate.edu/wiki/index.php/CS_500_Fall_2023 fall 2023], [https://cs.indstate.edu/wiki/index.php/CS_500_Spring_2023 spring 2023], [https://cs.indstate.edu/wiki/index.php/CS_500_Fall_2022 fall 2022]
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'''CS 510 Fast Track Introduction to Programming''' -
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[https://cs.indstate.edu/wiki/index.php/CS_510_Spring_2023 spring 2023], [https://cs.indstate.edu/wiki/index.php/CS_510_Fall_2022 fall 2022]
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'''CS 559 Topics in Computer Science''' -
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[http://cs.indstate.edu/~jkinne/cs559-f2013/ fall 2013]
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'''CS 609 Web Programming and Applications''' -
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[https://docs.google.com/document/d/1SSEoV9GVN2bufYw4Bf9cXnmwbMeq5IFqF6jX7SNH3vI/edit?usp=sharing fall 2015 (as CS 650-003)]
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'''CS 603 Networking and Security''' -
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[https://docs.google.com/document/d/1NAauNCjScp25i3Es0XUiKJRO38TdAEWeQ_m4D5N5LHs/edit?usp=sharing fall 2016]
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'''CS 617 Databases, Data Mining, and Big Data''' -
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[https://docs.google.com/document/d/1G_gtgO0f3fgNcV8qcQ_BOtrwQKMZ3uhCFO3psd6OusI/edit?usp=sharing fall 2017]
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'''CS 618 Computational Biology''' -
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[https://cs.indstate.edu/wiki/index.php/CS_618 summer 2024], [https://cs.indstate.edu/~jkinne/cs618-s2022 spring 2022]
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'''CS 620 Theory of Computation II''' -
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[https://docs.google.com/document/d/1ivvIzcExIW3rvdnxiL95cNwd0YHOhcFhhCwciCnHHA4/edit?usp=sharing  spring 2016],
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[http://cs.indstate.edu/~jkinne/cs620-s2011 spring 2011], [http://cs.indstate.edu/~jkinne/cs620-f2010 fall 2010]
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'''CS 658 Algorithms II''' -
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[http://cs.indstate.edu/~jkinne/cs658-s2014 spring 2014], [http://cs.indstate.edu/~jkinne/cs658-s2012 spring 2012]
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'''CS 670 Concurrent Programming''' -
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[http://cs.indstate.edu/~jkinne/cs670-s2021 spring 2021], [http://cs.indstate.edu/~jkinne/cs670-s2012 spring 2013]
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'''CS 671 Operating Systems II''' -
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[https://docs.google.com/document/d/1kJVEYJYOo7mZyz5GcasP890V3K6mLji6naDUFa4m4UQ/edit?usp=sharing spring 2017]
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'''CS 695 Computer Science Research''' -
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[https://docs.google.com/document/d/1L8doHFFBIgnNuZ38X-uOq2OnU8vWJTBeGUC2jXj0yzc/edit?usp=sharing fall 2014],
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[http://cs.indstate.edu/~jkinne/cs695-s2011 spring 2011]
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'''CS 399/699 Computer Science Internship''' -
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[https://docs.google.com/document/d/19IBirbzutL4ldaXIvKvzZHOMa9JULalt7clvvy0SDBk/edit?usp=sharing information]
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[http://cs.indstate.edu/~jkinne/bio491-f2014/ old bioinformatics stuff]
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===Wisconsin-Madison===
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'''CS/Math 240 Discrete Mathematics''' -  [http://pages.cs.wisc.edu/~jkinne/CS240-sum2007/ summer 2007]
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'''CS 810/710 Theory of Computation''' - [http://pages.cs.wisc.edu/~dieter/Courses/2007s-CS810 spring 2007]
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'''CS 310 Problem Solving with Computers''' - [http://pages.cs.wisc.edu/~hasti/cs310/ fall 2003 - spring 2005]
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=Other presentations=
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Other presentations I have given that I have saved...
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''Biology journal club at ISU'' on Oct 2, 2019. The intended audience are biology graduate students and faculty. The main goal of the talk is to do a detailed demo of the different ''tools used to process and analyze RNA sequence data'', with a focus on performing differential gene expression analysis. [https://docs.google.com/presentation/d/1oNM-eA0NlzaFhY5s5nDZqmyk3SVkhI2N3uUF8_DpOtg/edit?usp=sharing google slides].
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''CCSC Midwest'' (Consortium for Computing Sciences in Colleges) on Sept 29, 2018 at the 2018 . The talk gives the current ''status of K-12 CS education in the state of Indiana''. There were new state standards and resources available. It is a good time to be involved in CS Education in Indiana. [https://docs.google.com/presentation/d/1NVjVeq91qJ3UpeAlYrKmyVGtx2yIQPjA3A9lt2Nv8mE/edit#slide=id.p google slides].
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''Terre Haute Children's Museum K-4 Coding Camp'' on Jul 26, 2018. The basic format could work for any age K-8. [https://docs.google.com/presentation/d/1KtcMnQgTUsoFvKGxOGlOLtWa8Dypkyd7LhuF1K0z4Y0/edit?usp=sharing google slides].
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''Indiana Academy of Sciences'' on Mar 15, 2014. The goal of the talk was to give an overview of the ''records for largest known primes'', and a touch of the computation that goes into these computer searches. The intended audience is people who are interested in the topic (fairly broad). [http://cs.indstate.edu/~jkinne/talks/IAS-jkinne-2014.pdf PDF].
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''Midwest Theory Day'' on Nov 23, 2013. The goal of the talk was to give an overview of the ''techniques and theorems used in computational searches for the largest (provably) known prime numbers''. The intended audience is math and CS graduate students and faculty. [http://cs.indstate.edu/~jkinne/talks/MTD-jkinne-2013.pdf PDF].
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Capital University on Feb 4, 2013, Ohio Northern University on Feb 14, 2013, and Indiana State University on April 17. The goal of the talk was to introduce some ''research topics in the area of randomized algorithms and derandomization'' through some examples and considering the best algorithms known for primality testing. The intended audience was math and CS students. [http://cs.indstate.edu/~jkinne/talks/randAndDerand.pptx PPTx].
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''Panel discussion on undergraduate research'' at ISU on October 3, 2012 and October 9, 2012. The goal of the talk is to share my experiences with undergraduate research - as it applies to Math and CS students at ISU. The audience was an interdisciplinary group of faculty. [http://cs.indstate.edu/~jkinne/talks/undergradResearch.pdf PDF].
 +
 +
''Math and CS Department Seminar'' on March 21, 2012. The goal of the talk was to give an overview of some of the important ''results in lower bounds in theory of computing''. For many problems, we think they are intractable (require exponential time to solve), but this has not been proved yet. This talk looks at some things that are known. At the end is a mention of my own work in this area, but that is not the focus of the talk. [http://cs.indstate.edu/~jkinne/talks/lower-bounds-in-theory.pdf PDF].
 +
 +
''Rose Hulman Institute of Technology Mathematics Seminar'' on April 27, 2011. The goal with the talk was to give a flavor of the ''problems looked at within computational complexity'', how the problems are posed, some interesting results and open questions, ... The talk is aimed at a general audience with some knowledge of math and computer science. [https://docs.google.com/present/edit?id=0AbxM6icc2fOUZGhmM3FndzVfOTVnNmZubnBkMw&hl=en google doc].
 +
 +
''ISU Math and CS department seminar'' on February 11 and 25, 2011. A series of two talks on (1) an algebraic version of the P versus NP problem and (2) connections between obtaining algorithms for polynomial identity testing and lower bounds against algebraic P. The talk is aimed at a general audience who has some knowledge of math and computer science. [PPTx].
 +
 +
''Wabash College Math and CS department colloquium'' on November 16, 2010, on the ''P versus NP problem''. The talk is aimed at a general audience who has some knowledge of computer science. [http://cs.indstate.edu/~jkinne/talks/p-versus-np.ppt PPT].
 +
 +
''My "job talk" that I gave at Indiana State'' when I was applying for the job. This describes my research within the context of some of the major open questions in computer science. The intended audience is people with some knowledge of computer science. [http://cs.indstate.edu/~jkinne/talks/isu-job-talk.pdf PDF].
 +
 +
''Hot topics on theory of computing''. This talk, given in March of 2009 at UW-Madison, was given to a group of graduate students at UW-Madison who were on the job market. The idea was to give some flavor about what some of the topics are that theory researchers currently work on. [http://cs.indstate.edu/~jkinne/talks/theory-hot-topics.pdf PDF].
 +
 +
=Links=
 +
These are for my personal use, but I like to have them somewhere I can get to from anywhere.
 +
 +
'''News/Info:''' Terre Haute ([http://tribstar.com/ tribune star] | [http://www.mywabashvalley.com mywabashvalley]), [http://www.indystar.com Indianapolis] | [http://www.cincinnati.com Cincinnati] |
 +
[http://news.google.com Google News] ([https://news.google.com/home?hl=es-419&gl=US&ceid=US:es-419 es]) | [https://en.wikipedia.org/wiki/Main_Page Wikipedia] ([https://es.wikipedia.org/wiki/Wikipedia:Portada es]) | [https://www.bbc.com/mundo BBC Mundo]
 +
 +
'''Terre Haute/Indiana:''' weather ([http://forecast.weather.gov/MapClick.php?CityName=Terre+Haute&state=IN&site=IND&textField1=39.4704&textField2=-87.3835&e=0 NWS] | [https://www.windy.com/39.467/-87.414?38.988,-87.414,8 windy.com]) ([https://www.nws.noaa.gov/wtf/MapClick.php?CityName=Terre+Haute&state=IN&site=IND&textField1=39.4704&textField2=-87.3835&e=0&lg=sp es]) |
 +
[http://library.indstate.edu ISU library] | [http://www.vigo.lib.in.us/ Public Library]
 +
</p>
 +
 +
''Non-public:''
 +
[https://docs.google.com/spreadsheets/d/198I0idSJptzUU5wjQxrUIWQBgOYMgw_CrBvTDyrZY54/edit?usp=sharing Home repairs and bills] | [https://calendar.google.com Google Calendar]
 +
 +
''German:''    [https://en.wikibooks.org/wiki/German Wikibook] | [https://docs.google.com/document/d/1kFzWpnl4kiEYwYbFJs3MsqyRyDkIMEBosDMm7g3P9Dg/edit?usp=sharing notes]
 +
 +
''Astronomy:'' [http://www.skyandtelescope.com Sky and Telescope] | [http://www.heavens-above.com/?Loc=Terre+Haute&Lat=39.467&Lng=-87.414&Alt=138&TZ=EST Heavens Above Terre Haute] |
 +
[http://www.cleardarksky.com/c/TrrHtINkey.html?1 Terre Haute Clear Sky Chart] | [https://www.lightpollutionmap.info/ light pollution map] | [http://worldwidetelescope.org World Wide Telescope] | [http://media.skyandtelescope.com/documents/MullaneyDeepSky111.pdf 111 treasures for light-polluted skies (PDF)] | [http://www.keo.org/uk/pages/introuk.html Space Time Capsule] | [https://stellarium.org/ Stellarium] ([https://stellarium-web.org/ web]) | [https://www.spaceweatherlive.com/ SpaceWeatherLive]

Latest revision as of 15:43, 25 May 2024

This page is maintained by me, Jeff Kinne. I am a professor of computer science at Indiana State University. I have taught just about every CS course that we offer at the BS and MS levels. I was trained in computational complexity (within theoretical computer science) during my PhD studies and continue to be interested in this year. Since maybe 2015 or so, most of my research work has been in bioinformatics. If you want a laundry list of things I have done, you can see my C.V. (aka resume).

Contact

I am currently in the midst of moving from Root Hall to Technology Center at ISU. My email address will not change, and I believe my phone number should stay the same as well.

Email: jkinne@indstate.edu (also jkinne@cs.indstate.edu and jeffrey.kinne@indstate.edu all go to the same place).

Phone: office phone - 812-237-2126.

Office: within the ECET office suite, TC 301

Virtual meetings: ISU uses Teams and Zoom. I am happy to meet on other platforms as well (Google meet, WebEx, Skype, etc.).

Schedule a meeting: https://cs.indstate.edu/jkinne-meeting

Note: I use a separate email account for things not related to ISU and research (e.g., things having to do with my kids' school, scouts, etc.). If you're not sure what email address to use for me, feel free to use any that you have.

Research

Author ordering In CS and mathematics, author ordering is normally alphabetical (so you cannot tell who is the primary author just by looking at the author list). In biology / bioinformatics, author ordering is normally in order of who contributed the most - normally the primary author is listed first, and the director of the laboratory that paid for the research is listed last. Many papers published recently have a statement on author contributions (who did what, etc.) at the end of the paper.

Current projects Projects that I am still actively working on from among those listed below include: differential gene expression analysis, transcription factor binding site analysis, and gene expression analysis in cichlids. For other completed projects, there is always the possibility to improve the results or apply techniques to a new setting.

Posters

Differential gene expression analysis - 2022 BD4ISU/SURE, 2019 Indiana Academy of Sciences, 2019 ICIBM, 2019 BD4ISU/SURE, 2018 BD4ISU/SURE, 2018 SURF, 2018 SURE

Transcription factor binding site analysis - 2022 BD4ISU/SURE, 2019 BD4ISU/SURE

Transmembrane protein search in prokaryotes - 2021 BD4ISU/SURE

Predicting Drug-Gene Interactions - 2020 BD4ISU/SURE

Gene expression analysis in cichlids - 2021 BD4ISU/SURE, 2020 BD4ISU/SURE

3d printing - 2016 SURE

Large prime searches - (2014, 2013 SURE, 2013 CSUI

Publication list

Tara Hoffman, Jeff Kinne, Kyu Hong Cho. Pro-SMP finder-A systematic approach for discovering small membrane proteins in prokaryotes. PLoS One. 2024 Feb 29;19(2):e0299169. full text, pipeline.

Jeff Kinne, Akbar Rafiey, Arash Rafiey, Mohammad Sorkhpar. Vertex Ordering with Precedence Constraints. In: Fernau, H., Jansen, K. (eds) Fundamentals of Computation Theory. FCT 2023. Lecture Notes in Computer Science, vol 14292. Springer, Cham. DOI.

Nick Gabry, Jeff Kinne, and Rusty Gonser. MetaPlex: An Ion Torrent COI metabarcoding workflow and toolkit to increase experimental efficacy and efficiency. manuscript, source code.

Timothy J. Divoll, Veronica A. Brown, Jeff Kinne, Gary F. McCracken and Joy M. O'Keefe. Disparities in second-generation DNA metabarcoding results exposed with accessible and repeatable workflows. Molecular Ecology Resources, 2018. abstract, source code.

Yongsheng Bai, Jeff Kinne, Lizhong Ding, Ethan Rath, Aaron Cox, Siva Naidu and Youping Deng. Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly. BMC Bioinformatics, 18(Suppl 11):382, 2017. full text, presentation (for ugrad CS majors), source code, presented at ICIBM 2016.

Yongsheng Bai, Jeff Kinne, Brandon Donham, Feng Jiang, Lizhong Ding, Justin R. Hassler, and Randal J. Kaufman. Read-Split-Run: An improved bioinformatics pipeline for identification of genome-wide non-canonical spliced regions using RNA-Seq data. BMC Genomics 17(Suppl 7):503, 2016. full text, source code, presented at ICIBM 2015.

Ruiwen Chen, Valentine Kabanets, and Jeff Kinne. Lower Bounds against Weakly-Uniform Threshold Circuits. In special issue of Algorithmica for invited papers from the the 18th International Computing and Combinatorics Conference (COCOON), Volume 17, issue 1, pages 47-75, 2014, doi:10.1007/s00453-013-9823-y. draft PDF, ECCC report.

Jeff Kinne. On TC0 Lower Bounds for the Permanent. In Proceedings of the 18th International Computing and Combinatorics Conference (COCOON), LNCS 7434, pages 420-432, 2012. draft PDF, presentation.

George Karakostas, Jeff Kinne, Dieter van Melkebeek. On Derandomization and Average-Case Complexity of Monotone Functions. In Theoretical Computer Science, volume 434, pages 35-44, 2012. draft PDF

Jeff Kinne, Dieter van Melkebeek, and Ronen Shaltiel. Pseudorandom Generators, Typically-Correct Derandomization, and Circuit Lower Bounds. In the special issue of Computational Complexity for selected papers from The 13th International Workshop on Randomization and Computation (RANDOM), Volume 21, number 1, pages 3-61, 2012. draft PDF, ECCC report.

Jeff Kinne. Deterministic Simulations and Hierarchy Theorems for Randomized Algorithms. Ph.D. dissertation from the Computer Sciences department at the University of Wisconsin-Madison, 2010. PDF, presentation.

Jeff Kinne and Dieter van Melkebeek. Space Hierarchy Results for Randomized and Other Semantic Models. In Computational Complexity volume 19, number 3, 2010, pages 423-475. draft PDF, ECCC report.

Jeff Kinne, Dieter van Melkebeek, and Ronen Shaltiel. Pseudorandom Generators and Typically-Correct Derandomization. In Proceedings of the 13th International Workshop on Randomization and Computation (RANDOM), LNCS 5687, pages 574-587, 2009. PDF, presentation.

Jeff Kinne and Dieter van Melkebeek. Space Hierarchy Results for Randomized Models. In Proceedings of the 25th International Symposium on Theoretical Aspects of Computer Science (STACS), pages 433-444, 2008. PDF, presentation.

Teaching

For some of my recent thoughts on teaching, see teaching thoughts. I tend to update that once a year or few.

And here is the laundry list of links to course websites...

Indiana State University

Summer Honors (high school) - Arificial Intelligence (2017)

GH 101 Computing and Data Science - fall 2021, fall 2018

CS 151 Introduction to Programming - spring 2024, fall 2023, summer 2020, spring 2020, fall 2019, summer 2017 fall 2014, spring 2014, fall 2013, spring 2013 sections 001 and 003, fall 2012 section 001, spring 2012 sections 001 and 003, fall 2011 sections 001 and 002, spring 2011 section 003, fall 2010 section 003

CS 170 Web Programming I - Summer 2016

CS 201 Computer Science I - Summer 2016, spring 2015, spring 2014

CS 203 (formerly 303) Discrete Structures and Computing Theory - spring 2024, fall 2023, spring 2023, fall 2022,

CS 220 Java Programming - spring 2015

CS 302 (formerly 202) Computer Science II - fall 2020, fall 2019, fall 2017, spring 2017, spring 2016

CS 420/520 Theory of Computation - spring 2019, fall 2016, fall 2015

CS 440/540 Graphics Programming - fall 2012

CS 457/557 Database Processing - fall 2012

CS 458/558 Algorithms - fall 2020, fall 2013

CS 459/559 Topics in Computer Science - BD4ISU Summer 2019, BD4ISU Bioinformatics Programming, Spring 2019, Computational Software Packages and Tools, Summer I 2014

CS 469/569 Unix/Linux Administration and Networking - spring 2022

CS 471/571 Operating Systems - Fall 2018

CS 473/573 Computer Networks - fall 2021, spring 2021, spring 2020, spring 2015

CS 475/575 Artificial Intelligence - fall 2011

CS 499 Senior Seminar - fall 2020, fall 2019, information

CS 500 Programming Fundamentals - spring 2024, fall 2023, spring 2023, fall 2022

CS 510 Fast Track Introduction to Programming - spring 2023, fall 2022

CS 559 Topics in Computer Science - fall 2013

CS 609 Web Programming and Applications - fall 2015 (as CS 650-003)

CS 603 Networking and Security - fall 2016

CS 617 Databases, Data Mining, and Big Data - fall 2017

CS 618 Computational Biology - summer 2024, spring 2022

CS 620 Theory of Computation II - spring 2016, spring 2011, fall 2010

CS 658 Algorithms II - spring 2014, spring 2012

CS 670 Concurrent Programming - spring 2021, spring 2013

CS 671 Operating Systems II - spring 2017

CS 695 Computer Science Research - fall 2014, spring 2011

CS 399/699 Computer Science Internship - information

old bioinformatics stuff

Wisconsin-Madison

CS/Math 240 Discrete Mathematics - summer 2007

CS 810/710 Theory of Computation - spring 2007

CS 310 Problem Solving with Computers - fall 2003 - spring 2005

Other presentations

Other presentations I have given that I have saved...

Biology journal club at ISU on Oct 2, 2019. The intended audience are biology graduate students and faculty. The main goal of the talk is to do a detailed demo of the different tools used to process and analyze RNA sequence data, with a focus on performing differential gene expression analysis. google slides.

CCSC Midwest (Consortium for Computing Sciences in Colleges) on Sept 29, 2018 at the 2018 . The talk gives the current status of K-12 CS education in the state of Indiana. There were new state standards and resources available. It is a good time to be involved in CS Education in Indiana. google slides.

Terre Haute Children's Museum K-4 Coding Camp on Jul 26, 2018. The basic format could work for any age K-8. google slides.

Indiana Academy of Sciences on Mar 15, 2014. The goal of the talk was to give an overview of the records for largest known primes, and a touch of the computation that goes into these computer searches. The intended audience is people who are interested in the topic (fairly broad). PDF.

Midwest Theory Day on Nov 23, 2013. The goal of the talk was to give an overview of the techniques and theorems used in computational searches for the largest (provably) known prime numbers. The intended audience is math and CS graduate students and faculty. PDF.

Capital University on Feb 4, 2013, Ohio Northern University on Feb 14, 2013, and Indiana State University on April 17. The goal of the talk was to introduce some research topics in the area of randomized algorithms and derandomization through some examples and considering the best algorithms known for primality testing. The intended audience was math and CS students. PPTx.

Panel discussion on undergraduate research at ISU on October 3, 2012 and October 9, 2012. The goal of the talk is to share my experiences with undergraduate research - as it applies to Math and CS students at ISU. The audience was an interdisciplinary group of faculty. PDF.

Math and CS Department Seminar on March 21, 2012. The goal of the talk was to give an overview of some of the important results in lower bounds in theory of computing. For many problems, we think they are intractable (require exponential time to solve), but this has not been proved yet. This talk looks at some things that are known. At the end is a mention of my own work in this area, but that is not the focus of the talk. PDF.

Rose Hulman Institute of Technology Mathematics Seminar on April 27, 2011. The goal with the talk was to give a flavor of the problems looked at within computational complexity, how the problems are posed, some interesting results and open questions, ... The talk is aimed at a general audience with some knowledge of math and computer science. google doc.

ISU Math and CS department seminar on February 11 and 25, 2011. A series of two talks on (1) an algebraic version of the P versus NP problem and (2) connections between obtaining algorithms for polynomial identity testing and lower bounds against algebraic P. The talk is aimed at a general audience who has some knowledge of math and computer science. [PPTx].

Wabash College Math and CS department colloquium on November 16, 2010, on the P versus NP problem. The talk is aimed at a general audience who has some knowledge of computer science. PPT.

My "job talk" that I gave at Indiana State when I was applying for the job. This describes my research within the context of some of the major open questions in computer science. The intended audience is people with some knowledge of computer science. PDF.

Hot topics on theory of computing. This talk, given in March of 2009 at UW-Madison, was given to a group of graduate students at UW-Madison who were on the job market. The idea was to give some flavor about what some of the topics are that theory researchers currently work on. PDF.

Links

These are for my personal use, but I like to have them somewhere I can get to from anywhere.

News/Info: Terre Haute (tribune star | mywabashvalley), Indianapolis | Cincinnati | Google News (es) | Wikipedia (es) | BBC Mundo

Terre Haute/Indiana: weather (NWS | windy.com) (es) | ISU library | Public Library

Non-public: Home repairs and bills | Google Calendar

German: Wikibook | notes

Astronomy: Sky and Telescope | Heavens Above Terre Haute | Terre Haute Clear Sky Chart | light pollution map | World Wide Telescope | 111 treasures for light-polluted skies (PDF) | Space Time Capsule | Stellarium (web) | SpaceWeatherLive

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